Environmental DNA
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Environmental DNA or eDNA is
In recent years, eDNA has been used as a tool to detect endangered wildlife that were otherwise unseen. In 2020, human health researchers began repurposing eDNA techniques to track the COVID-19 pandemic.[3]
Example sources of eDNA include, but are not limited to,
The analysis of eDNA has great potential, not only for monitoring common species, but to genetically detect and identify other extant species that could influence conservation efforts.[7] This method allows for biomonitoring without requiring collection of the living organism, creating the ability to study organisms that are invasive, elusive, or endangered without introducing anthropogenic stress on the organism. Access to this genetic information makes a critical contribution to the understanding of population size, species distribution, and population dynamics for species not well documented. Importantly, eDNA is often more cost-effective compared to traditional sampling methods.[8] The integrity of eDNA samples is dependent upon its preservation within the environment.
Soil,
On 7 December 2022, The New York Times reported that two-million year old eDNA genetic material was found in Greenland, and is currently considered the oldest DNA discovered so far.[11][12]
Overview
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Global ecosystem and biodiversity monitoring
with environmental DNA metabarcoding [6]
Environmental DNA or eDNA describes the genetic material present in environmental samples such as sediment, water, and air, including whole cells, extracellular DNA and potentially whole organisms.[13][14] The analyse of eDNA start with capturing an environmental sample of interest. The DNA in the sample is extracted and purified. The purified DNA is then amplified for a specific gene target so it can be sequenced and categorised based on its sequence.[15] From this information, detection and classification of species is possible.[6]
eDNA can come from skin, mucous, saliva, sperm, secretions, eggs, feces, urine, blood, roots, leaves, fruit, pollen, and rotting bodies of larger organisms, while microorganisms may be obtained in their entirety.[16][7][14] eDNA production is dependent on biomass, age and feeding activity of the organism as well as physiology, life history, and space use.[2][17][14][18][19][6]
Despite being a relatively new method of surveying, eDNA has already proven to have enormous potential in
Degradation of eDNA in the environment limits the scope of eDNA studies, as often only small segments of genetic material remain, particularly in warm, tropical regions. Additionally, the varying lengths of time to degradation based on environmental conditions and the potential of DNA to travel throughout media such as water can affect inference of fine-scale spatiotemporal trends of species and communities.[17][22][16][23][18][20][19] Despite these drawbacks, eDNA still has the potential to determine relative or rank abundance as some studies have found it to correspond with biomass, though the variation inherent in environmental samples makes it difficult to quantify.[7][14] While eDNA has numerous applications in conservation, monitoring, and ecosystem assessment, as well as others yet to be described, the highly variable concentrations of eDNA and potential heterogeneity through the water body makes it essential that the procedure is optimized, ideally with a pilot study for each new application to ensure that the sampling design is appropriate to detect the target.[24][18][20][6]
Community DNA
While the definition of eDNA seems straightforward, the lines between different forms of DNA become blurred, particularly in comparison to
selfDNA
The concept of selfDNA stems from discoveries made by scientists from the
eDNA metabarcoding
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Applications of environmental DNA metabarcoding in aquatic and terrestrial ecosystems [6]
By 2019 methods in eDNA research had been expanded to be able to assess whole communities from a single sample. This process involves
eDNA metabarcoding has applications to diversity monitoring across all habitats and taxonomic groups, ancient ecosystem reconstruction,
Extracellular and relic DNA
-
Relic DNA dynamics [39]
Extracellular DNA, sometimes called relic DNA, is DNA from dead microbes. Naked extracellular DNA (eDNA), most of it released by cell death, is nearly ubiquitous in the environment. Its concentration in soil may be as high as 2 μg/L, and its concentration in natural aquatic environments may be as high at 88 μg/L.[40] Various possible functions have been proposed for eDNA: it may be involved in horizontal gene transfer;[41] it may provide nutrients;[42] and it may act as a buffer to recruit or titrate ions or antibiotics.[43] Extracellular DNA acts as a functional extracellular matrix component in the biofilms of several bacterial species. It may act as a recognition factor to regulate the attachment and dispersal of specific cell types in the biofilm;[44] it may contribute to biofilm formation;[45] and it may contribute to the biofilm's physical strength and resistance to biological stress.[46]
Under the name of environmental DNA, eDNA has seen increased use in the natural sciences as a survey tool for ecology, monitoring the movements and presence of species in water, air, or on land, and assessing an area's biodiversity.[47][48]
In the diagram on the right, the amount of relic DNA in a microbial environment is determined by inputs associated with the mortality of viable individuals with intact DNA and by losses associated with the degradation of relic DNA. If the diversity of sequences contained in the relic DNA pool is sufficiently different from that in the intact DNA pool, then relic DNA may bias estimates of microbial biodiversity (as indicated by different colored boxes) when sampling from the total (intact + relic) DNA pool.[39] Standardised Data on Initiatives (STARDIT) has been proposed as one way of standardising both data about sampling and analysis methods, and taxonomic and ontological relationships.[49]
Collection
Terrestrial sediments
-
(a) Metabarcoding is the amplification and analysis of equally sized DNA fragments from a total DNA extract. (b) Metagenomics is the extraction, amplification, and analysis of all DNA fragments independent of size. (c) Target-capture describes the enrichment and analysis of specific (chosen) DNA fragments independent of size from a total DNA extract.[50]
The importance of eDNA analysis stemmed from the recognition of the limitations presented by culture-based studies.[7] Organisms have adapted to thrive in the specific conditions of their natural environments. Although scientists work to mimic these environments, many microbial organisms can not be removed and cultured in a laboratory setting.[9] The earliest version of this analysis began with ribosomal RNA (rRNA) in microbes to better understand microbes that live in hostile environments.[51] The genetic makeup of some microbes is then only accessible through eDNA analysis. Analytical techniques of eDNA were first applied to terrestrial sediments yielding DNA from both extinct and extant mammals, birds, insects and plants.[52] Samples extracted from these terrestrial sediments are commonly referenced as 'sedimentary ancient DNA' (sedaDNA or dirtDNA).[53] The eDNA analysis can also be used to study current forest communities including everything from birds and mammals to fungi and worms.[9] Samples can be obtained from soil, faeces, 'bite DNA' from where leaves have been bitten, plants and leaves where animals have been, and from the blood meals of captured mosquitos which may have eaten blood from any animals in the area.[54] Some methods can also attempt to capture cells with hair traps and sandpaper in areas commonly transversed by target species.
Aquatic sediments
The sedaDNA was subsequently used to study ancient animal diversity and verified using known fossil records in aquatic sediments.[9] The aquatic sediments are deprived of oxygen and are thus protect the DNA from degrading.[9] Other than ancient studies, this approach can be used to understand current animal diversity with relatively high sensitivity. While typical water samples can have the DNA degrade relatively quickly, the aquatic sediment samples can have useful DNA two months after the species was present.[55] One problem with aquatic sediments is that it is unknown where the organism deposited the eDNA as it could have moved in the water column.
-
Drilling vessel recovering a sediment core for sedaDNA analysis and hypothetical past marine community composition [50]
-
Subglacial aquatic sediment continuous coring [56]
Aquatic (water column)
Studying eDNA in the water column can indicate the community composition of a body of water. Before eDNA, the main ways to study open water diversity was to use fishing and trapping, which requires resources such as funding and skilled labour, whereas eDNA only needs samples of water.[10] This method is effective as pH of the water does not affect the DNA as much as previously thought, and sensitivity can be increased relatively easily.[10][57] Sensitivity is how likely the DNA marker will be present in the sampled water, and can be increased simply by taking more samples, having bigger samples, and increasing PCR.[57] eDNA degrades relatively fast in the water column, which is very beneficial in short term conservation studies such as identifying what species are present.[9]
Researchers at the Experimental Lakes Area in Ontario, Canada and McGill University have found that eDNA distribution reflects lake stratification.[58] As seasons and water temperature change, water density also changes such that it forms distinct layers in small boreal lakes in the summer and winter. These layers mix during the spring and fall.[59] Fish habitat use correlates to stratification (e.g. a cold-water fish like lake trout will stay in cold water) and so does eDNA distribution, as these researchers found.[58]
Monitoring species
eDNA can be used to monitor species throughout the year and can be very useful in conservation monitoring.[17][60][61] eDNA analysis has been successful at identifying many different taxa from aquatic plants,[62] aquatic mammals,[21][17] fishes,[32][61] mussels,[60] fungi [63][64] and even parasites.[65][51] eDNA has been used to study species while minimizing any stress inducing human interaction, allowing researchers to monitor species presence at larger spatial scales more efficiently.[66][67] The most prevalent use in current research is using eDNA to study the locations of species at risk, invasive species, and keystone species across all environments.[66] eDNA is especially useful for studying species with small populations because eDNA is sensitive enough to confirm the presence of a species with relatively little effort to collect data which can often be done with a soil sample or water sample.[7][66] eDNA relies on the efficiency of genomic sequencing and analysis as well as the survey methods used which continue to become more efficient and cheaper.[68] Some studies have shown that eDNA sampled from stream and inshore environment decayed to undetectable level at within about 48 hours.[69][70]
Environmental DNA can be applied as a tool to detect low abundance organisms in both active and passive forms. Active eDNA surveys target individual species or groups of taxa for detection by using highly sensitive species-specific quantitative real-time PCR[71] or digital droplet PCR markers.[72] CRISPR-Cas methodology has also been applied to the detection of single species from eDNA;[73] utilising the Cas12a enzyme and allowing greater specificity when detecting sympatric taxa. Passive eDNA surveys employ massively-parallel DNA sequencing to amplify all eDNA molecules in a sample with no a priori target in mind providing blanket DNA evidence of biotic community composition.[74]
Decline of terrestrial arthropods
-
Tanacetum vulgare).[1]
Terrestrial
Terrestrial arthropod communities have traditionally been collected and studied using methods, such as
Mammals
-
Canada lynx
-
Tracks of a Canada lynx in snow
Snow tracks
Wildlife researchers in snowy areas also use snow samples to gather and extract genetic information about species of interest. DNA from snow track samples has been used to confirm the presence of such elusive and rare species as polar bears, arctic fox, lynx, wolverines, and fishers.[111][112][113][114]
DNA from the air
In 2021, researchers demonstrated that eDNA can be collected from air and used to identify mammals.[115][116][117][118] In 2023, scientists developed a specialized sampling probe and aircraft surveys to assess biodiversity of multiple taxa, including mammals, using air eDNA.[119]
Managing fisheries
The successful
Environmental DNA (eDNA) has emerged as a potentially powerful alternative for studying ecosystem dynamics. The constant loss and shedding of genetic material from macroorganisms imparts a molecular footprint in environmental samples that can be analysed to determine either the presence of specific target species [13][127] or characterise biodiversity.[128][129] The combination of next generation sequencing and eDNA sampling has been successfully applied in aquatic systems to document spatial and temporal patterns in the diversity of fish fauna.[130][131][132][133] To further develop the utility of eDNA for fisheries management, understanding the ability of eDNA quantities to reflect fish biomass in the ocean is an important next step.[126]
Positive relationships between eDNA quantities and
Despite these potential constraints, numerous studies in
Deep sea sediments
-
OTU (operational taxonomic unit) network of the extracellular DNA pools from the sediments of the different continental margins.[148]
Extracellular DNA in surface deep-sea sediments is by far the largest reservoir of DNA of the world oceans.[149] The main sources of extracellular DNA in such ecosystems are represented by in situ DNA release from dead benthic organisms, and/or other processes including cell lysis due to viral infection, cellular exudation and excretion from viable cells, virus decomposition, and allochthonous inputs from the water column.[149][150][151][152] Previous studies provided evidence that an important fraction of extracellular DNA can escape degradation processes, remaining preserved in the sediments.[153][154] This DNA represents, potentially, a genetic repository that records biological processes occurring over time.[155][156][148]
Recent investigations revealed that DNA preserved in marine sediments is characterized by a large number of highly diverse gene sequences.[155][156][157] In particular, extracellular DNA has been used to reconstruct past prokaryotic and eukaryotic diversity in benthic ecosystems characterized by low temperatures and/or permanently anoxic conditions.[157][158][159][160][161][148]
The diagram on the right shows the OTU (operational taxonomic unit) network of the extracellular DNA pools from the sediments of the different continental margins. The dot size within the network is proportional to the abundance of sequences for each OTU. Dots circled in red represent extracellular core OTUs, dot circled in yellow are partially shared (among two or more pools) OTUs, dots circled in black are OTUs exclusive of each pool. The core OTUs contributing at least for 20 sequences are shown. The numbers in parentheses represent the number of connections among OTUs and samples: 1 for exclusive OTUs, 2–3 for partially shared OTUs and 4 for core OTUs.[148]
Previous studies suggested that the preservation of DNA might be also favoured in benthic systems characterised by high organic matter inputs and sedimentation rates, such as continental margins.[162][163] These systems, which represent ca. 15% of the global seafloor, are also hotspots of benthic prokaryotic diversity,[164][165][166] and therefore they could represent optimal sites to investigate the prokaryotic diversity preserved within extracellular DNA.[148]
Spatial distribution of prokaryotic diversity has been intensively studied in benthic deep-sea ecosystems [167][168][169][170] through the analysis of "environmental DNA" (i.e., the genetic material obtained directly from environmental samples without any obvious signs of biological source material).[9] However, the extent to which gene sequences contained within extracellular DNA can alter the estimates of the diversity of the present-day prokaryotic assemblages is unknown.[171][148]
Sedimentary ancient DNA
Analyses of
Despite the long exposure to degradation under
Planktonic foraminifera sedaDNA is an ideal proxy both “horizontally” to assess the spatial resolution of reconstructing past surface ocean hydrographic features and “vertically”, to unambiguously track the burial of its signal throughout the sediment column. Indeed, the flux of planktonic foraminifera eDNA should be proportionate to the flux of dead foraminiferal shells sinking to the seafloor, allowing independent benchmarking of the eDNA signal. eDNA is powerful tool to study ecosystem because it does not require direct taxonomic knowledge thus allowing information to be gathered on every organism present in a sample, even at the
In 2022, two-million year old eDNA genetic material was discovered and sequenced in Greenland, and is currently considered the oldest DNA discovered so far.[11][12]
Participatory research and citizen science
The relative simplicity of eDNA sampling lends itself to projects which seek to involve local communities in being part of research projects, including collecting and analysing DNA samples. This can empower local communities (including Indigenous peoples) to be actively involved in monitoring the species in an environment, and help make informed decisions as part of participatory action research model. An example of such a project has been demonstrated by the charity Science for All with the 'Wild DNA' project.[195]
See also
- Circulating free DNA
- Exogenous DNA
- Extracellular RNA
- RNAs present in environmental samples
- Shadow Effect (Genetics)
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Further references
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